oligo 1.40.2
Benilton Carvalho
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/oligo | | Last Changed Rev: 131492 / Revision: 131943 | | Last Changed Date: 2017-07-21 14:08:19 -0400 (Fri, 21 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings oligo_1.40.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/oligo.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.40.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oligo’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 29.6Mb
sub-directories of 1Mb or more:
doc 12.9Mb
scripts 15.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
partial argument match of 'nr' to 'nrow'
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
partial argument match of 'nc' to 'ncol'
NUSE: no visible global function definition for ‘abline’
RLE: no visible global function definition for ‘abline’
basicMvApairsPlot: no visible binding for global variable
‘smoothScatter’
basicMvApairsPlot: no visible global function definition for ‘frame’
basicMvApairsPlot: no visible global function definition for ‘text’
basicMvApairsPlot: no visible global function definition for ‘IQR’
basicMvApairsPlot: no visible global function definition for ‘mtext’
basicMvAplot: no visible binding for global variable ‘smoothScatter’
basicMvAplot: no visible global function definition for ‘IQR’
basicMvAplot: no visible global function definition for ‘loess’
basicMvAplot: no visible global function definition for ‘approx’
basicMvAplot: no visible global function definition for ‘abline’
basicMvAplot: no visible global function definition for ‘text’
fitAffySnpMixture: no visible global function definition for
‘aggregate’
getRefDABG: no visible global function definition for ‘data’
invariantsetV: no visible global function definition for
‘smooth.spline’
invariantsetV: no visible global function definition for ‘approx’
loessNormV: no visible global function definition for ‘loess’
loessNormV: no visible global function definition for ‘predict’
maplot: no visible binding for global variable ‘smoothScatter’
qsplineNorm: no visible global function definition for ‘smooth.spline’
qsplineNorm: no visible global function definition for ‘splinefun’
MAplot,ExpressionSet: no visible binding for global variable
‘smoothScatter’
MAplot,FeatureSet: no visible binding for global variable
‘smoothScatter’
MAplot,TilingFeatureSet: no visible binding for global variable
‘smoothScatter’
MAplot,TilingFeatureSet: no visible global function definition for
‘rnorm’
MAplot,matrix: no visible binding for global variable ‘smoothScatter’
backgroundCorrect,matrix: no visible binding for global variable
‘intensities’
pmFragmentLength,AffySNPPDInfo: no visible global function definition
for ‘complete.cases’
pmindex,GenericPDInfo: no visible binding for global variable
‘man_fsetid’
Undefined global functions or variables:
IQR abline aggregate approx complete.cases data frame intensities
loess man_fsetid mtext predict rnorm smooth.spline smoothScatter
splinefun text
Consider adding
importFrom("graphics", "abline", "frame", "mtext", "smoothScatter",
"text")
importFrom("stats", "IQR", "aggregate", "approx", "complete.cases",
"loess", "predict", "rnorm", "smooth.spline", "splinefun")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'boxplot':
\S4method{boxplot}{FeatureSet}
Code: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
= log2, nsample = 10000, target = "mps1", ...)
Docs: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
= log2, nsample = 10000, ...)
Argument names in code not in docs:
target
Mismatches in argument names:
Position: 5 Code: target Docs: ...
Codoc mismatches from documentation object 'hist':
\S4method{hist}{FeatureSet}
Code: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
"all"), nsample = 10000, target = "mps1", ...)
Docs: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
"all"), nsample = 10000, ...)
Argument names in code not in docs:
target
Mismatches in argument names:
Position: 5 Code: target Docs: ...
S4 class codoc mismatches from documentation object 'oligoPLM-class':
Slots for class 'oligoPLM'
Code: annotation chip.coefs description geometry manufacturer method
narrays nprobes nprobesets phenoData probe.coefs protocolData
residualSE residuals se.chip.coefs se.probe.coefs weights
Docs: annotation chip.coefs geometry manufacturer method narrays
nprobes nprobesets probe.coefs residualSE residuals
se.chip.coefs se.probe.coefs weights
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
‘Makefile’
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 23.768 0.056 23.870
getProbeInfo 11.672 0.432 12.340
fitProbeLevelModel 5.376 0.020 5.624
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 7 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/oligo.Rcheck/00check.log’
for details.
* installing *source* package ‘oligo’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c DABG.c -o DABG.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types]
while (!gzeof(file)){
^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1475:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzeof OF((gzFile file));
^
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
gzgets(file, buffer, 1000);
^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
fp = gzopen(currentFile, "rb");
^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
gzgets(fp, buffer, LINEMAX);
^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(fp);
^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(fp);
^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer, LINEMAX, fp);
^
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(buffer, LINEMAX, fp);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (oligo)